What governments will still be standing and what new governments will rise? Because I don't think humans now on the pony planet are just going to swear fealty to princess Luna or whatever leader of what ever land they happen to be in. The same being true with Neighbors accepting human rule. Here is a couple of my proposals.

Earth:
The Neo-Equestrian Empire - After hearing stories of sightings of a gold armored Neighbor (my general term for all the beings now on earth) in the state of Wyoming, several ponies flocked there, hoping that Celestia will once again take charge and end the crisis. While Celestia refused to take up the crown once more, her actions secured Pony rule over the former state of Wyoming and several neighboring states. At the end of the Cosmic Crisis, Celestia's niece Cadence took up the Crown and formed the Neo-Equestrian Empire.

The Republic of Texas - With the United States slowly dissolving under the Cosmic Crisis, Texas seceded from the union and absorbs the US forces stationed there in the their military. Despite lacking most of the resources the United States had, Texas was successful in repelling Neighbor forces out the state. Many wandering neighbors during the duration of the Crisis did well the avoid the Lone Star State.

4130034 Two things: Celestia will be spending a lot of time in and around the state of Wyoming, for she has found a soon-to-be important person there.

Secondly, Texas is one of the most successful militia states, seeing as how just under 36% of the population owns guns and aren't shy in using them.

Just thought I'd throw those out there.

4168726 I meant Wyoming when I posted this, I don't know how I got those two mixed up fixed it now.

And that's why I propose Texas become its' own independent nation for this setting. Though it lacks Nuclear weapons and the like, just as you said a lot of people own guns.

4168817 Good ol' Texas. Yeehaw.

Sounds like a cool idea I am once more wanting to start more on my own trans cosmic story but I want to conclude my other story aswell. But good luck with writing everybody

4168820 I also forgot to mention (technically I didn't) that Texas has its own military. On an unrelated note, I can picture the concept of this universe crossing over with your universe once everything has calmed down.

4175790 Maybe for an AU, but not canon. There are too many discrepancies between the two for a realistic melding, though I don't doubt the novelty of a human lover (or the opposite, for humans) is going to cause quite a few to find attraction with the new species ppresented.

4178683 I can also picture our women now in the pony planet (are you gonna name it Equis or are you going to name it somthing else) getting the worse of the civil unrest that will be unfolding. With much higher female population on the pony world, Human women would probably be harnessed for so much as looking at a stallion.

Anyway back on topic, would Luna just have a set of land to be a human reservation or will the humans now in the pony world have pledge allegence or swear fealty to her or who ever ruler in the lands they happen to be in.

4178996 Luna and Celestia both ironed out the details before the merge even began. Knowing Celestia as she's portrayed, what do you believe will happen?

Side-note: while humans aren't going to be outright imprisoned, they are going to find the other world to be quite different. First of all, they'll have to come to terms with the fact that they're no longer the only sapient being around -- that alone is going to take some time to digest -- and for the most part, they're physically inferior. While Equestrians were prepared for the arrival of the humans, they won't have any problem laying the smack down on any human that tries to intimidate or take control of a world that isn't theirs. All of the allied races have been advised of everything Twilight saw regarding humans, so they're prepared for the groups of people who are going to attempt to take advantage of the situation for their own benefit.

4182468 Knowing Celestia, she's going to take a very militaristic approach to handling things and would probably be considered the most wanted person alive and would be betrayed by noble griffons, minotaurs, even noble ponies now on earth.

Side Comment: I like the story and all, but so far, you make it sound like that humanity is practically helpless in this situation. It would be nice for human both in Earth and the pony world to have a good amount of leverage against the neighbors and even humans doing things not even Twilight foreseen.

4216789 Humanity has its technology, but said technology comes at the price of having to make it. In many ways, humans are technologically superior to any race the mirror world has to offer -- vastly so, in most cases -- but that offsets a lack of natural ability. So you see, humans aren't as strong or quick as the new races, but they have technologies that, while they take time to make, brings them on par or above the skills and abilities many of the other races have.

For example: while it's true humans aren't able to kill a dragon without massive collateral damage, they have the means to incapacitate and/or imprison them.

As far as Celestia, she's going to have a fair bit of backlash sent her way because she has rescinded her crown in favor of a non-royal life, but there's no doubt that she's respected for her many years of service to Equestria and its allies. She won't easily be betrayed, and nor are any that have known her prepared to take such a risk with the amount of social, political and economical pull she will still wield, regardless of her social status. Any who try and attempt some sort of coup would likely be those who believe she's become a betrayer to her own world, and though many were understanding of her stance, not all were.